Equality of the branches

The Constitution does not explicitly indicate the pre-eminence of any particular branch of government. However, James Madison wrote in Federalist 51, regarding the ability of each branch to defend itself from actions by the others, that "it is not possible to give to each department an equal power of self-defense. In republican government, the legislative authority necessarily predominates."
One may claim that the judiciary has historically been the weakest of the three branches. In fact, its power to exercise judicial review — its sole meaningful check on the other two branches — is not explicitly granted by the U.S. Constitution. The U.S. Supreme Court exercised its power to strike down congressional acts as unconstitutional only twice prior to the Civil War: in Marbury v. Madison (1803) and Dred Scott v. Sandford (1857). While the Supreme Court has since then made more extensive use of judicial review, it cannot be said to have as much political power as either Congress or the President.
Throughout America's history dominance of one of the three branches has essentially been a see-saw struggle between congress and the president. Both have had periods of great power and weakness such as immediately after the Civil War when republicans had a majority in congress and were able to pass major legislation and shoot down most of the president's vetoes. They also passed acts to essentially make the president subordinate to congress, such as the Tenure of Office Act. Johnson's later impeachment also cost the presidency much political power. However the president has also exercised greater power largely during the 20th century. Both Roosevelts greatly expanded the powers of the president and wielded great power during their terms. Johnson and Nixon during the 1960s and 1970s exploited the presidency particularly Nixon.
The first six presidents of the United States did not make extensive use of the veto power: George Washington only vetoed two bills, James Monroe one, and John Adams, Thomas Jefferson and John Quincy Adams none. James Madison, a firm believer in a strong executive, vetoed seven bills. None of the first six Presidents, however, used the veto to direct national policy. It was Andrew Jackson, the seventh President, who was the first to use the veto as a political weapon. During his two terms in office, he vetoed twelve bills—more than all of his predecessors combine

. Furthermore, he defied the Supreme Court in enforcing the policy of ethnically cleansing Native American tribes ("Indian Removal"); he stated, "John Marshall has made his decision. Now let him enforce it!"
Some of Jackson's successors made no use of the veto power, while others used it intermittently. It was only after the Civil War that presidents began to use the power to truly counterbalance Congress. Andrew Johnson, a Democrat, vetoed several Reconstruction bills passed by the "Radical Republicans." Congress, however, managed to override fifteen of Johnson's twenty-nine vetoes. Furthermore, it attempted to curb the power of the presidency by passing the Tenure of Office Act. The Act required Senate approval for the dismissal of senior Cabinet officials. When Johnson deliberately violated the Act, which he felt was unconstitutional (Supreme Court decisions later vindicated such a position), the House of Representatives impeached him; he was acquitted in the Senate by one vote.
Grover Cleveland worked to restore power to the Presidency after Andrew Johnson's impeachment.
Johnson's impeachment was perceived to have done great damage to the presidency, which came to be almost subordinate to Congress. Some believed that the president would become a mere figurehead, with the Speaker of the House of Representatives becoming a de facto Prime Minister. Grover Cleveland, the first Democratic President following Johnson, attempted to restore the power of his office. During his first term, he vetoed over four hundred bills—twice as many bills as his twenty-one predecessors combined. He also began to suspend bureaucrats who were appointed as a result of the patronage system, replacing them with more "deserving" individuals. The Senate, however, refused to confirm many new nominations, instead demanding that Cleveland turn over the confidential records relating to the suspensions. Cleveland steadfastly refused, asserting, "These suspensions are my executive acts ... I am not responsible to the Senate, and I am unwilling to submit my actions to them for judgment." Cleveland's popular support forced the Senate to back down and confirm the nominees. Furthermore, Congress finally repealed the controversial Tenure of Office Act that had been passed during the Johnson Administration. Overall, this meant that Cleveland's Administration marked the end of presidential subordination.